Summary 1. An experiment was carried out to determine whether the community composition of root-colonizing arbuscular mycorrhizal fungi (AMF) influences the growth and nutrient status of two congeneric Pulsatilla species, one rare and one common in Estonia. We hypothesized that: (i) establishment and growth of plants is influenced by the composition of native AMF communities; (ii) growth of congeneric plant species with different abundances differs due to their response to specific AMF communities; and (iii) distribution of a plant species may depend on the composition of local root symbiotic AMF communities. 2. Rare Pulsatilla patens and common Pulsatilla pratensis were grown in pots, under homogeneous soil nutrient and microbial community conditions, containing either one from two (grassland and forest sites) of natural AMF soil inocula, or no AMF. 3. Lower establishment was observed in the non-mycorrhizal soil compared to AMF inoculated soils. Plant biomass, phosphorus concentration and root AMF colonization of both species were higher, and nitrogen concentration lower, in grassland as opposed to forest inoculum. 4. The common species displayed more vigorous growth than the rare counterpart in the presence of grassland inoculum. Conversely, slightly better growth of a rare species was recorded in the forest inoculum, in which plant biomass was an order of magnitude lower compared to the grassland inoculum. 5. As Pulsatilla spp. roots hosted site-characteristic AMF small-subunit rDNA sequence groupings, we suggest that the presence of AM fungi that are more beneficial for the common species may be one factor behind the observed differential distribution and performance of the two plant species.